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1805: Coronavirus Spike Protein Binder Design
Status: Closed

Summary

Name: 1805: Coronavirus Spike Protein Binder Design
Status: Closed
Created: 02/27/2020
Points: 0
Expired: 03/05/2020 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle was closed early because some tools were unintentioally disabled; the puzzle has been reposted as Puzzle 1805b. Players may load solutions into the reposted Puzzle 1805b.

Design a binder against coronavirus! In late 2019, a new highly-infections virus emerged out of Wuhan, China. This virus belongs to the coronavirus family, and is similar to the virus that caused the SARS epidemic in 2002. Coronaviruses display a "spike" protein on their surface, which binds tightly to a receptor protein found on the surface of human cells. Once the coronavirus spike binds to the human receptor, the virus can infect the human cell and replicate. In recent weeks, researchers have determined the structure of the 2019 coronavirus spike protein and how it binds to human receptors. If we can design a protein that binds to this coronavirus spike protein, it could be used to block the interaction with human cells and halt infection!

In this puzzle, players are presented with the binding site of the coronavirus spike protein. The backbone and most of the sidechains are completely frozen, except for sidechains at the binding site, where the spike protein normally interacts with the human receptor protein. Players can design a new protein that binds to these sidechains, blocking interactions with the human receptor. In order to bind the coronavirus target, designs will need to make lots of contacts and H-bonds with the spike protein at this binding site. But designs will also need to have lots of secondary structure (helices or sheets) and a large core, so that they fold up correctly! See the puzzle comments for Objective details.
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Comments

bkoep's picture
User offline. Last seen 15 min 50 sec ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Residue Count (max +550)
Penalizes extra residues inserted beyond the starting 192, at a cost of 55 points per residue. Players may use up to 202 residues in total.

Core Existence (max +2400)
Ensures that at least 28 percent of residues are buried in the core of the monomer unit.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

alcor29's picture
User offline. Last seen 2 hours 36 min ago. Offline
Joined: 11/16/2012
No blueprint?

Seems to me that would be a big help here.

spvincent's picture
User offline. Last seen 3 hours 27 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Agrred. It's almost essential

Agrred. It's almost essential for the Ideal Loop Filter.

bkoep's picture
User offline. Last seen 15 min 50 sec ago. Offline
Joined: 11/15/2012
Groups: None
Good catch!

This puzzle has been closed and reposted as Puzzle 1805b, with the Blueprint tool enabled.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons